Researchers forge new computational tools to make more accurate predictions of protein structures | 6/6/2018 | Staff
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Where the village smithy once stood now stands an algorithm, its mighty mathematical hammer pounding proteins into shape.

The blacksmith's profession is a worthy analogy for what Rice University scientists have wrought: A new method for making accurate structural models of proteins that takes far less computational power than existing brute-force approaches.

Goal - Models - Computation - Physicist - Peter

The goal of the structural models produced by computation, according to physicist Peter Wolynes of Rice's Center for Theoretical Biological Physics (CTBP), is to be as detailed and useful as those produced by laborious experimental means, particularly X-ray crystallography, that provide detailed locations for every atom within a protein.

The new method takes its inspiration from metallurgy. Like the blacksmith who must not only heat and cool a metal but also strike the metal just right to move it closer to a useful product, the Rice project led by Wolynes and alumnus Xingcheng Lin applies force at strategic points during the simulation of protein models so as to speed up the computation.

Question - Accuracy - Results - Simulation - Result

"One big question is whether we could ever become more confident in the accuracy of the results of a simulation than the result of X-ray experiments," Wolynes said. "I'm on the verge of saying that's where we are now but, of course, time will tell."

The study appears this week in the Proceedings of the National Academy of Sciences.Researchers have used X-ray crystallography for more than a century to learn the positions of atoms within molecules from their structures in protein crystals. This information is the starting point for structural biology studies, and accuracy is thought to be essential for designing drugs to interact with specific proteins.

Structures - Snapshot - Protein - Reality - Changes

But crystal structures provide only a snapshot of a protein that in reality changes its global shape and detailed atomic positions as the protein carries out its work in the cell.

Wolynes and his colleagues have...
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